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- PDB-1ckm: STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME I... -

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Basic information

Entry
Database: PDB / ID: 1ckm
TitleSTRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP
ComponentsMRNA CAPPING ENZYME
KeywordsCAPPING ENZYME / MRNA / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding
Similarity search - Function
mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Few Secondary Structures ...mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / mRNA-capping enzyme
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH A MERCURY DERIVATIVE OBTAINED BY SOAKING THE CRYSTAL FOR TWO HOURS IN 1 MM THIMEROSAL, A SELENOMETHIONINE DERIVATIVE / Resolution: 2.5 Å
AuthorsHakansson, K. / Doherty, A.J. / Wigley, D.B.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.
Authors: Hakansson, K. / Doherty, A.J. / Shuman, S. / Wigley, D.B.
#1: Journal: To be Published
Title: Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1 Change During Guanyl Transfer by Mrna Capping Enzymes
Authors: Doherty, A.J. / Hakansson, K. / Ho, C.K. / Shuman, S. / Wigley, D.B.
History
DepositionApr 20, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MRNA CAPPING ENZYME
B: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8164
Polymers75,7702
Non-polymers1,0462
Water6,485360
1
A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4082
Polymers37,8851
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4082
Polymers37,8851
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: MRNA CAPPING ENZYME
B: MRNA CAPPING ENZYME
hetero molecules

A: MRNA CAPPING ENZYME
B: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,6338
Polymers151,5404
Non-polymers2,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12320 Å2
ΔGint-24 kcal/mol
Surface area54630 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-8 kcal/mol
Surface area28810 Å2
MethodPISA
5
A: MRNA CAPPING ENZYME
hetero molecules

A: MRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8164
Polymers75,7702
Non-polymers1,0462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4410 Å2
ΔGint-8 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.332, 214.931, 105.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE IN DIFFERENT CONFORMATIONS. THE PROTEIN IS MONOMERIC AND THIS ENTRY MERELY REPRESENTS A CO-CRYSTAL OF THE ENZYME IN TWO DIFFERENT CONFORMATIONS.

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Components

#1: Protein MRNA CAPPING ENZYME / RNA GUANYLYLTRANSFERASE


Mass: 37884.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q84424, mRNA guanylyltransferase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST ...Details: HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: unknown / Details: Doherty, A.J., (1996) Nucl. Acids Res., 24. 2281.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 U/mlclostripain11
250 mMTris-HCl11
35 mM11CaCl2
45 mMdithiothreitol11
510 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.448 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 36196 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR WITH A MERCURY DERIVATIVE OBTAINED BY SOAKING THE CRYSTAL FOR TWO HOURS IN 1 MM THIMEROSAL, A SELENOMETHIONINE DERIVATIVE
Resolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.299 -5 %
Rwork0.218 --
obs0.218 35714 97.5 %
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 64 360 5546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.714
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.16
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLUSER DEFINED
X-RAY DIFFRACTION3USER DEFINED
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.164
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.99

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